updated checkm to 1.2.3

[erinyoung]

There's a new version of checkm!

According to the release notes, there is better handling of non-zero return codes and support for numpy 2.0.

I think this is a low priority PR.

HHMER, prodigal, and pplacer do not have new versions.

Although the diff makes it look like I made a lot of changes, I didn't change much.

Changes:

1. Updated the version ARG
2. Added version to pip install checkm-genome
3. Separated pplacer install to a new RUN layer
4. Adjusted tabs and spacing (notably &&/ -> && /)

The full diff

$ diff checkm/1.2.*/Dockerfile
3c3
< ARG CHECKM_VER="1.2.2"
---
> ARG CHECKM_VER="1.2.3"
11c11
< LABEL website="dockerfile-template/Dockerfile dockerfile-template/README.md"
---
> LABEL website="https://github.com/Ecogenomics/CheckM"
22c22
<     prodigal &&\
---
>     prodigal && \
26,28c26,31
< RUN pip install --no-cache-dir numpy matplotlib pysam checkm-genome &&\
<     wget https://github.com/matsen/pplacer/releases/download/${PPLACER_VER}/pplacer-linux-${PPLACER_VER}.zip && \
<     unzip pplacer-linux-${PPLACER_VER}.zip && rm pplacer-linux-${PPLACER_VER}.zip
---
> RUN pip install --no-cache-dir numpy matplotlib pysam checkm-genome==${CHECKM_VER}
> 
> # download pplacer
> RUN wget -q https://github.com/matsen/pplacer/releases/download/${PPLACER_VER}/pplacer-linux-${PPLACER_VER}.zip && \
>     unzip pplacer-linux-${PPLACER_VER}.zip && \
>     rm pplacer-linux-${PPLACER_VER}.zip
41a45,46
> RUN checkm -h
> 
43,44c48,50
< RUN wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz &&\
<     mkdir checkm_db && tar -C checkm_db -xvf checkm_data_2015_01_16.tar.gz &&\
---
> RUN wget -q https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz && \
>     mkdir checkm_db && \
>     tar -C checkm_db -xvf checkm_data_2015_01_16.tar.gz && \

Pull Request (PR) checklist:

• [X] Include a description of what is in this pull request in this message.
• [X] The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15 )
• [X] Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number (i.e. spades/3.12.0/Dockerfile)
  • [X] (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
• [X] Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
  • [X] If this README is longer than 30 lines, there is an explanation as to why more detail was needed
• [X] Dockerfile includes the recommended LABELS
• [X] Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• [X] Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

[Kincekara]

Thank you for the update! Deploy link: https://github.com/StaPH-B/docker-builds/actions/runs/9893437903